problem in coloring a selected region

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Manish Manish

10 Sep 2011 10 Sep '11

3:16 a.m.

Dear Chimera Developer,

I want to select a region in protein molecule and then color.

I have open a pdb file 1HA0 (attached), and then select a sequence TQNGGSNACKR (attached image) then color in blue (attached image). But this colors non selected part.

I am using ubuntu 11.04 natty, VGA compatible controller: Intel Corporation Core Processor Integrated Graphics Controller (rev 18) Subsystem: Dell Device 0447 Kernel driver in use: i915 Kernel modules: i915

and Chimera 1.5.3 .

Regards Manish

Attachments:

attachment.html (text/html — 606 bytes)
selcted_region.png (image/png — 216.6 KB)
selected_region_colored_blue.png (image/png — 219.8 KB)
1HA0.pdb (chemical/x-pdb — 40 bytes)

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Elaine Meng

10 Sep 10 Sep

3:32 a.m.

Hi Manish, I was unable to reproduce this problem, at least using the Mac version (both 1.5.3 and current daily build).

I opened 1ha0, menu: Select... Sequence and entered TQNGGSNACKR, then menu: Actions... Color... blue. Only the selected part was colored blue. You could also do Favorites... Sequence to show the whole sequence and then select that part by dragging a box on that part of the sequence.

After selecting, you could also try command: color blue sel

...instead of using the menu, but it is really doing the same thing. Also, I see those residues are 131 to 141, so yet another way is to use the command: color blue :131-141

If you still have trouble, however, please use "Help... Report a Bug" in the menu to report the problem. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Sep 9, 2011, at 8:16 PM, Manish Manish wrote:

...

Dear Chimera Developer,

I want to select a region in protein molecule and then color.

I have open a pdb file 1HA0 (attached), and then select a sequence TQNGGSNACKR (attached image) then color in blue (attached image). But this colors non selected part.

I am using ubuntu 11.04 natty, VGA compatible controller: Intel Corporation Core Processor Integrated Graphics Controller (rev 18) Subsystem: Dell Device 0447 Kernel driver in use: i915 Kernel modules: i915

and Chimera 1.5.3 .

Regards Manish

Greg Couch

5:27 a.m.

This might be an issue with your graphics driver. The Intel graphics drivers are much better than they used to be, but they still have many problems. If you have the option of installing an AMD/ATI or NVIDIA graphics card and the corresponding proprietary driver, you'll be much happier.

-- Greg

On 9/9/2011 8:16 PM, Manish Manish wrote:

...

Dear Chimera Developer,

I want to select a region in protein molecule and then color.

I have open a pdb file 1HA0 (attached), and then select a sequence TQNGGSNACKR (attached image) then color in blue (attached image). But this colors non selected part.

I am using ubuntu 11.04 natty, VGA compatible controller: Intel Corporation Core Processor Integrated Graphics Controller (rev 18) Subsystem: Dell Device 0447 Kernel driver in use: i915 Kernel modules: i915

and Chimera 1.5.3 .

Regards Manish

Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Manish Manish

5:42 a.m.

Thanks a lot Greg and Elaine, I will for opt other graphics.

Regards Manish On Fri, Sep 9, 2011 at 10:27 PM, Greg Couch gregc@cgl.ucsf.edu wrote:

...

This might be an issue with your graphics driver. The Intel graphics drivers are much better than they used to be, but they still have many problems. If you have the option of installing an AMD/ATI or NVIDIA graphics card and the corresponding proprietary driver, you'll be much happier.
-- Greg
On 9/9/2011 8:16 PM, Manish Manish wrote:

Dear Chimera Developer,

I want to select a region in protein molecule and then color.

I have open a pdb file 1HA0 (attached), and then select a sequence TQNGGSNACKR (attached image) then color in blue (attached image). But this colors non selected part.

I am using ubuntu 11.04 natty, VGA compatible controller: Intel Corporation Core Processor Integrated Graphics Controller (rev 18) Subsystem: Dell Device 0447 Kernel driver in use: i915 Kernel modules: i915

and Chimera 1.5.3 .

Regards Manish

Chimera-users mailing listChimera-users@cgl.ucsf.eduhttp://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hernando J Sosa

20 Oct 20 Oct

5:33 p.m.

New subject: Intel graphics?

Dear Chimera Developers/Users I'm curious if it is still the case that Intel graphic drivers are not very good to run chimera. I've been looking for a laptop replacement and some of the options I am considering (e.g. Samsung series 9) come with Intel graphics only (Intel HD Graphics 3000).

Thanks

Hernando

From: chimera-users-bounces@cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Manish Manish Sent: Saturday, September 10, 2011 1:43 AM To: Greg Couch Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] problem in coloring a selected region

Thanks a lot Greg and Elaine, I will for opt other graphics.

Regards Manish On Fri, Sep 9, 2011 at 10:27 PM, Greg Couch <gregc@cgl.ucsf.edumailto:gregc@cgl.ucsf.edu> wrote: This might be an issue with your graphics driver. The Intel graphics drivers are much better than they used to be, but they still have many problems. If you have the option of installing an AMD/ATI or NVIDIA graphics card and the corresponding proprietary driver, you'll be much happier.

-- Greg

On 9/9/2011 8:16 PM, Manish Manish wrote: Dear Chimera Developer,

I want to select a region in protein molecule and then color.

I have open a pdb file 1HA0 (attached), and then select a sequence TQNGGSNACKR (attached image) then color in blue (attached image). But this colors non selected part.

and Chimera 1.5.3 .

Regards Manish

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Chimera-users mailing list

Chimera-users@cgl.ucsf.edumailto:Chimera-users@cgl.ucsf.edu

http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edumailto:Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Greg Couch

7:15 p.m.

New subject: Intel graphics?

The Intel HD Graphics 3000 is much better than previous Intel offerings and the Intel's OpenGL drivers have improved considerably too. That said, personally, I would get laptop with AMD/ATI Radeon or Nvidia GeForce graphics, but the Samsung series 9 should be more than adequate. If you get one, please run Chimera's Tools / Utilities / Benchmark tool and submit the results, so the Chimera benchmark page, http://www.cgl.ucsf.edu/trac/chimera/wiki/benchmarks, will show the relative performance.

-- Greg

On 10/20/2011 10:33 AM, Hernando J Sosa wrote:

...

Dear Chimera Developers/Users

I'm curious if it is still the case that Intel graphic drivers are not very good to run chimera. I've been looking for a laptop replacement and some of the options I am considering (e.g. Samsung series 9) come with Intel graphics only (Intel HD Graphics 3000).

Thanks

Hernando

//

*/From:/*/chimera/-users-bounces@cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] *On Behalf Of *Manish Manish *Sent:* Saturday, September 10, 2011 1:43 AM *To:* Greg Couch *Cc:* chimera-users@cgl.ucsf.edu *Subject:* Re: [Chimera-users] problem in coloring a selected region

Thanks a lot Greg and Elaine, I will for opt other graphics.

Regards Manish

On Fri, Sep 9, 2011 at 10:27 PM, Greg Couch <gregc@cgl.ucsf.edu mailto:gregc@cgl.ucsf.edu> wrote:

This might be an issue with your graphics driver. The Intel graphics drivers are much better than they used to be, but they still have many problems. If you have the option of installing an AMD/ATI or NVIDIA graphics card and the corresponding proprietary driver, you'll be much happier.
-- Greg
On 9/9/2011 8:16 PM, Manish Manish wrote:
Dear Chimera Developer,

I want to select a region in protein molecule and then color.

I have open a pdb file 1HA0 (attached), and then select a sequence
TQNGGSNACKR (attached image)
then color in blue (attached image). But this colors non selected
part.

I am using ubuntu 11.04 natty,
VGA compatible controller: Intel Corporation Core Processor
Integrated Graphics Controller (rev 18)
    Subsystem: Dell Device 0447
    Kernel driver in use: i915
    Kernel modules: i915

and Chimera 1.5.3 .

Regards
Manish

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Chimera-users mailing list

Chimera-users@cgl.ucsf.edu  <mailto:Chimera-users@cgl.ucsf.edu>

http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Elaine Meng
Greg Couch
Hernando J Sosa
Manish Manish